ArticleInternational journal of molecular sciences2021
Analyzing Low-Level mtDNA Heteroplasmy-Pitfalls and Challenges from Bench to Benchmarking.
Article in International journal of molecular sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Long-read sequencing enables high-accuracy mitochondrial heteroplasmy detection in Parkinson's disease.BMC genomics · 2026Article
- Umi-pipeline-nf: a modular and scalable workflow for UMI-tagged nanopore amplicon analysis with real-time sequencing integration and GPU-acceleration.Bioinformatics (Oxford, England) · 2026Article
- Pervasive non-random mitochondrial DNA heteroplasmy in the hybrid water frog Pelophylax esculentus.BMC ecology and evolution · 2025Article
- The quality and detection limits of mitochondrial heteroplasmy by long read nanopore sequencing.Scientific reports · 2024Article
- The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems.Journal of applied genetics · 2024Article
- mtDNA-Server 2: advancing mitochondrial DNA analysis through highly parallelized data processing and interactive analytics.Nucleic acids research · 2024Article
- Nanobiopsy investigation of the subcellular mtDNA heteroplasmy in human tissues.Scientific reports · 2024Article
- Assessing the feasibility of free DNA for disaster victim identification and forensic applications.Scientific reports · 2024Article
- Mitochondrial point heteroplasmy: insights from deep-sequencing of human replicate samples.BMC genomics · 2024Article
- Mitochondrial DNA Variants at Low-Level Heteroplasmy and Decreased Copy Numbers in Chronic Kidney Disease (CKD) Tissues with Kidney Cancer.International journal of molecular sciences · 2023Article
- Next-generation sequencing reveals mitogenome diversity in plasma extracellular vesicles from colorectal cancer patients.BMC cancer · 2023Article
- Benchmarking Low-Frequency Variant Calling With Long-Read Data on Mitochondrial DNA.Frontiers in genetics · 2022Article
- Benchmarking the Effectiveness and Accuracy of Multiple Mitochondrial DNA Variant Callers: Practical Implications for Clinical Application.Frontiers in genetics · 2022Article
- From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel.International journal of molecular sciences · 2021Article
- mtDNA Heteroplasmy: Origin, Detection, Significance, and Evolutionary Consequences.Life (Basel, Switzerland) · 2021Review
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Massive parallel sequencing technologies are promising a highly sensitive detection of low-level mutations, especially in mitochondrial DNA (mtDNA) studies. However, processes from DNA extraction and library construction to bioinformatic analysis include several varying tasks. Further, there is no validated recommendation for the comprehensive procedure. In this study, we examined potential pitfalls on the sequencing results based on two-person mtDNA mixtures. Therefore, we compared three DNA polymerases, six different variant callers in five mixtures between 50% and 0.5% variant allele frequencies generated with two different amplification protocols. In total, 48 samples were sequenced on Illumina MiSeq. Low-level variant calling at the 1% variant level and below was performed by comparing trimming and PCR duplicate removal as well as six different variant callers. The results indicate that sensitivity, specificity, and precision highly depend on the investigated polymerase but also vary based on the analysis tools. Our data highlight the advantage of prior standardization and validation of the individual laboratory setup with a DNA mixture model. Finally, we provide an artificial heteroplasmy benchmark dataset that can help improve somatic variant callers or pipelines, which may be of great interest for research related to cancer and aging.
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